Interpretive Summary: This significant work provides new information that grapevine rupestris stem pitting is associated with a complex of variant strains of the virus. This article provides sequence information on these variants, and adds towards unravelling the effect that these strains have on the severity of the disease. Since the disease is widespread in grapevines, this information will have practical impact on grapevine certification program for the US and the world.

Technical Abstract:
Grapevine rupestris stem pitting-associated virus (GRSPaV), a member of Foveavirus within Flexiviridae, is the putative causal agent of the disease Rupestris stem pitting (RSP) of grapevines. GRSPaV comprise a family of variants, whose pathological characteristics have not been determined. Recently, many of the indicator 'St. George' plants (Vitis rupestris) used throughout the world to index RSP tested positive for GRSPaV. This finding questions the validity of past biological indexing results. In this work, we first sequenced a representative genomic region of GRSPaV from 10 'St. George' plants from two sources and demonstrated that nine of them carried a new variant, GRSPaV-SG1. The genomes of GRSPaV-SG1 and GRSPaV-BS from 'Bertille Seyve 5563' are sequenced, revealing a genome structure identical to GRSPaV-1. Lastly, we experimentally demonstrate that infection of 'St. George' with GRSPaV-SG1 is asymptomatic and propose that GRSPaV-SG1 infection should have not interfered the outcome of past indicator indexing. To our knowledge, this represents the first attempt to link a GRSPaV variant with pathological properties.